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Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-37 (G206S, R207T, D210S)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 6000, 0,2 M MgCl2 in 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.224 α = 90 b = 74.112 β = 90 c = 147.766 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL RIGAKU HyPix-6000HE 2020-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 20.281 95.6 0.079 0.097 0.992 9 2.6 42970
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 89.8 0.327 0.487 0.702 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZAL 1.9 20.281 42929 1055 94.978 0.224 0.2228 0.2285 0.2883 0.2972 14.575
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.523 0.376 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.093 r_dihedral_angle_4_deg 18.365 r_dihedral_angle_3_deg 14.621 r_dihedral_angle_1_deg 7.283 r_lrange_it 3.729 r_lrange_other 3.701 r_angle_refined_deg 1.657 r_angle_other_deg 1.439 r_scangle_it 1.327 r_scangle_other 1.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.093 r_dihedral_angle_4_deg 18.365 r_dihedral_angle_3_deg 14.621 r_dihedral_angle_1_deg 7.283 r_lrange_it 3.729 r_lrange_other 3.701 r_angle_refined_deg 1.657 r_angle_other_deg 1.439 r_scangle_it 1.327 r_scangle_other 1.327 r_mcangle_it 1.269 r_mcangle_other 1.269 r_scbond_it 0.813 r_scbond_other 0.813 r_mcbond_it 0.732 r_mcbond_other 0.729 r_nbd_other 0.281 r_symmetry_nbd_refined 0.273 r_symmetry_xyhbond_nbd_refined 0.217 r_xyhbond_nbd_refined 0.21 r_nbd_refined 0.208 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.159 r_metal_ion_refined 0.152 r_symmetry_xyhbond_nbd_other 0.119 r_ncsr_local_group_1 0.105 r_ncsr_local_group_2 0.097 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.077 r_xyhbond_nbd_other 0.037 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4252 Nucleic Acid Atoms Solvent Atoms 526 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing